null Sun 23 Dec 22:22:56 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zbt-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zbt-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:06 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zbt-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 322 and 0 Target number of residues in the AU: 322 Target solvent content: 0.6390 Checking the provided sequence file Detected sequence length: 371 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 371 Adjusted target solvent content: 0.58 Input MTZ file: 1zbt-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 96 Cell parameters: 71.823 71.823 187.134 90.000 90.000 90.000 Input sequence file: 1zbt-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2968 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 28.608 3.600 Wilson plot Bfac: 71.44 6146 reflections ( 99.68 % complete ) and 0 restraints for refining 3293 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3342 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3660 (Rfree = 0.000) for 3293 atoms. Found 21 (21 requested) and removed 25 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.11 Search for helices and strands: 0 residues in 0 chains, 3331 seeds are put forward Round 1: 162 peptides, 24 chains. Longest chain 21 peptides. Score 0.425 Round 2: 195 peptides, 21 chains. Longest chain 28 peptides. Score 0.567 Round 3: 191 peptides, 22 chains. Longest chain 26 peptides. Score 0.543 Round 4: 196 peptides, 21 chains. Longest chain 29 peptides. Score 0.569 Round 5: 218 peptides, 21 chains. Longest chain 28 peptides. Score 0.626 Taking the results from Round 5 Chains 21, Residues 197, Estimated correctness of the model 24.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6146 reflections ( 99.68 % complete ) and 5461 restraints for refining 2472 atoms. 4694 conditional restraints added. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3162 (Rfree = 0.000) for 2472 atoms. Found 15 (15 requested) and removed 36 (7 requested) atoms. Cycle 2: After refmac, R = 0.3241 (Rfree = 0.000) for 2389 atoms. Found 15 (15 requested) and removed 35 (7 requested) atoms. Cycle 3: After refmac, R = 0.2875 (Rfree = 0.000) for 2342 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 4: After refmac, R = 0.2917 (Rfree = 0.000) for 2318 atoms. Found 15 (15 requested) and removed 21 (7 requested) atoms. Cycle 5: After refmac, R = 0.2830 (Rfree = 0.000) for 2297 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.08 Search for helices and strands: 0 residues in 0 chains, 2429 seeds are put forward Round 1: 181 peptides, 27 chains. Longest chain 22 peptides. Score 0.443 Round 2: 187 peptides, 23 chains. Longest chain 26 peptides. Score 0.518 Round 3: 216 peptides, 26 chains. Longest chain 26 peptides. Score 0.561 Round 4: 204 peptides, 21 chains. Longest chain 38 peptides. Score 0.591 Round 5: 213 peptides, 24 chains. Longest chain 19 peptides. Score 0.577 Taking the results from Round 4 Chains 21, Residues 183, Estimated correctness of the model 11.1 % 2 chains (47 residues) have been docked in sequence ------------------------------------------------------ 6146 reflections ( 99.68 % complete ) and 4977 restraints for refining 2519 atoms. 4071 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2928 (Rfree = 0.000) for 2519 atoms. Found 16 (16 requested) and removed 35 (8 requested) atoms. Cycle 7: After refmac, R = 0.2824 (Rfree = 0.000) for 2466 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 8: After refmac, R = 0.2655 (Rfree = 0.000) for 2432 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 9: After refmac, R = 0.2575 (Rfree = 0.000) for 2416 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 10: After refmac, R = 0.2491 (Rfree = 0.000) for 2402 atoms. Found 13 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 3.07 Search for helices and strands: 0 residues in 0 chains, 2478 seeds are put forward Round 1: 189 peptides, 25 chains. Longest chain 24 peptides. Score 0.496 Round 2: 190 peptides, 21 chains. Longest chain 23 peptides. Score 0.553 Round 3: 195 peptides, 22 chains. Longest chain 22 peptides. Score 0.554 Round 4: 210 peptides, 24 chains. Longest chain 23 peptides. Score 0.569 Round 5: 200 peptides, 25 chains. Longest chain 23 peptides. Score 0.529 Taking the results from Round 4 Chains 24, Residues 186, Estimated correctness of the model 2.2 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6146 reflections ( 99.68 % complete ) and 5561 restraints for refining 2651 atoms. 4744 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2820 (Rfree = 0.000) for 2651 atoms. Found 17 (17 requested) and removed 45 (8 requested) atoms. Cycle 12: After refmac, R = 0.2806 (Rfree = 0.000) for 2587 atoms. Found 16 (16 requested) and removed 33 (8 requested) atoms. Cycle 13: After refmac, R = 0.2773 (Rfree = 0.000) for 2547 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 14: After refmac, R = 0.2772 (Rfree = 0.000) for 2522 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. Cycle 15: After refmac, R = 0.2714 (Rfree = 0.000) for 2498 atoms. Found 16 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.04 Search for helices and strands: 0 residues in 0 chains, 2638 seeds are put forward Round 1: 160 peptides, 25 chains. Longest chain 17 peptides. Score 0.403 Round 2: 198 peptides, 24 chains. Longest chain 30 peptides. Score 0.536 Round 3: 197 peptides, 25 chains. Longest chain 19 peptides. Score 0.520 Round 4: 196 peptides, 25 chains. Longest chain 20 peptides. Score 0.517 Round 5: 202 peptides, 25 chains. Longest chain 21 peptides. Score 0.534 Taking the results from Round 2 Chains 25, Residues 174, Estimated correctness of the model 0.0 % 2 chains (40 residues) have been docked in sequence ------------------------------------------------------ 6146 reflections ( 99.68 % complete ) and 5199 restraints for refining 2615 atoms. 4375 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2733 (Rfree = 0.000) for 2615 atoms. Found 16 (16 requested) and removed 38 (8 requested) atoms. Cycle 17: After refmac, R = 0.2606 (Rfree = 0.000) for 2562 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 18: After refmac, R = 0.2575 (Rfree = 0.000) for 2538 atoms. Found 15 (16 requested) and removed 15 (8 requested) atoms. Cycle 19: After refmac, R = 0.2476 (Rfree = 0.000) for 2527 atoms. Found 15 (16 requested) and removed 19 (8 requested) atoms. Cycle 20: After refmac, R = 0.2467 (Rfree = 0.000) for 2519 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.10 Search for helices and strands: 0 residues in 0 chains, 2598 seeds are put forward Round 1: 157 peptides, 24 chains. Longest chain 14 peptides. Score 0.408 Round 2: 180 peptides, 24 chains. Longest chain 17 peptides. Score 0.483 Round 3: 178 peptides, 23 chains. Longest chain 17 peptides. Score 0.491 Round 4: 199 peptides, 26 chains. Longest chain 17 peptides. Score 0.513 Round 5: 196 peptides, 26 chains. Longest chain 21 peptides. Score 0.504 Taking the results from Round 4 Chains 26, Residues 173, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6146 reflections ( 99.68 % complete ) and 5646 restraints for refining 2684 atoms. 4916 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2778 (Rfree = 0.000) for 2684 atoms. Found 17 (17 requested) and removed 26 (8 requested) atoms. Cycle 22: After refmac, R = 0.2777 (Rfree = 0.000) for 2652 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 23: After refmac, R = 0.2752 (Rfree = 0.000) for 2610 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 24: After refmac, R = 0.2804 (Rfree = 0.000) for 2587 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 25: After refmac, R = 0.2718 (Rfree = 0.000) for 2564 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.11 Search for helices and strands: 0 residues in 0 chains, 2691 seeds are put forward Round 1: 155 peptides, 26 chains. Longest chain 15 peptides. Score 0.370 Round 2: 178 peptides, 26 chains. Longest chain 14 peptides. Score 0.448 Round 3: 177 peptides, 23 chains. Longest chain 16 peptides. Score 0.488 Round 4: 186 peptides, 25 chains. Longest chain 19 peptides. Score 0.487 Round 5: 195 peptides, 25 chains. Longest chain 19 peptides. Score 0.514 Taking the results from Round 5 Chains 25, Residues 170, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6146 reflections ( 99.68 % complete ) and 5916 restraints for refining 2682 atoms. 5261 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2964 (Rfree = 0.000) for 2682 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 27: After refmac, R = 0.2766 (Rfree = 0.000) for 2635 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 28: After refmac, R = 0.2805 (Rfree = 0.000) for 2607 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 29: After refmac, R = 0.2794 (Rfree = 0.000) for 2578 atoms. Found 16 (16 requested) and removed 17 (8 requested) atoms. Cycle 30: After refmac, R = 0.2807 (Rfree = 0.000) for 2567 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.44 3.09 Search for helices and strands: 0 residues in 0 chains, 2701 seeds are put forward Round 1: 152 peptides, 26 chains. Longest chain 13 peptides. Score 0.360 Round 2: 171 peptides, 24 chains. Longest chain 14 peptides. Score 0.455 Round 3: 171 peptides, 21 chains. Longest chain 22 peptides. Score 0.498 Round 4: 175 peptides, 23 chains. Longest chain 14 peptides. Score 0.482 Round 5: 183 peptides, 20 chains. Longest chain 23 peptides. Score 0.547 Taking the results from Round 5 Chains 22, Residues 163, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6146 reflections ( 99.68 % complete ) and 5443 restraints for refining 2670 atoms. 4666 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2833 (Rfree = 0.000) for 2670 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 32: After refmac, R = 0.2675 (Rfree = 0.000) for 2621 atoms. Found 15 (17 requested) and removed 13 (8 requested) atoms. Cycle 33: After refmac, R = 0.2578 (Rfree = 0.000) for 2605 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 34: After refmac, R = 0.2518 (Rfree = 0.000) for 2584 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 35: After refmac, R = 0.2434 (Rfree = 0.000) for 2585 atoms. Found 12 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.07 Search for helices and strands: 0 residues in 0 chains, 2654 seeds are put forward Round 1: 161 peptides, 26 chains. Longest chain 12 peptides. Score 0.391 Round 2: 181 peptides, 26 chains. Longest chain 22 peptides. Score 0.458 Round 3: 185 peptides, 22 chains. Longest chain 20 peptides. Score 0.525 Round 4: 194 peptides, 27 chains. Longest chain 16 peptides. Score 0.484 Round 5: 195 peptides, 26 chains. Longest chain 20 peptides. Score 0.501 Taking the results from Round 3 Chains 24, Residues 163, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6146 reflections ( 99.68 % complete ) and 5469 restraints for refining 2675 atoms. 4750 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2722 (Rfree = 0.000) for 2675 atoms. Found 17 (17 requested) and removed 32 (8 requested) atoms. Cycle 37: After refmac, R = 0.2633 (Rfree = 0.000) for 2636 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 38: After refmac, R = 0.2550 (Rfree = 0.000) for 2617 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. Cycle 39: After refmac, R = 0.2435 (Rfree = 0.000) for 2607 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 40: After refmac, R = 0.2378 (Rfree = 0.000) for 2602 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.06 Search for helices and strands: 0 residues in 0 chains, 2686 seeds are put forward Round 1: 167 peptides, 29 chains. Longest chain 14 peptides. Score 0.366 Round 2: 189 peptides, 30 chains. Longest chain 18 peptides. Score 0.426 Round 3: 196 peptides, 28 chains. Longest chain 18 peptides. Score 0.476 Round 4: 182 peptides, 24 chains. Longest chain 20 peptides. Score 0.489 Round 5: 187 peptides, 26 chains. Longest chain 16 peptides. Score 0.476 Taking the results from Round 4 Chains 26, Residues 158, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 6146 reflections ( 99.68 % complete ) and 5834 restraints for refining 2691 atoms. 5199 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2736 (Rfree = 0.000) for 2691 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 42: After refmac, R = 0.2708 (Rfree = 0.000) for 2667 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 43: After refmac, R = 0.2842 (Rfree = 0.000) for 2655 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 44: After refmac, R = 0.2811 (Rfree = 0.000) for 2643 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 45: After refmac, R = 0.2706 (Rfree = 0.000) for 2630 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.43 3.08 Search for helices and strands: 0 residues in 0 chains, 2749 seeds are put forward Round 1: 122 peptides, 23 chains. Longest chain 14 peptides. Score 0.296 Round 2: 164 peptides, 27 chains. Longest chain 16 peptides. Score 0.387 Round 3: 168 peptides, 23 chains. Longest chain 18 peptides. Score 0.460 Round 4: 166 peptides, 22 chains. Longest chain 17 peptides. Score 0.468 Round 5: 172 peptides, 23 chains. Longest chain 23 peptides. Score 0.472 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 149, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 1zbt-3_warpNtrace.pdb as input Building loops using Loopy2018 23 chains (149 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6146 reflections ( 99.68 % complete ) and 5758 restraints for refining 2659 atoms. 5156 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2733 (Rfree = 0.000) for 2659 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2889 (Rfree = 0.000) for 2629 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2942 (Rfree = 0.000) for 2607 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2883 (Rfree = 0.000) for 2585 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:13:49 GMT 2018 Job finished. TimeTaking 50.89 Used memory is bytes: 11564024